Mitigating methane (CH₄) emissions from paddy fields without compromising yield remains a critical challenge for sustainable agriculture, primarily due to trade-offs between emission reduction and nutrient availability. Biochar-based fertilizer (BF), which integrates biochar with mineral nutrients, may address this constraint by regulating carbon and nitrogen availability. This study evaluated the effects of biochar-based fertilization on CH₄ emissions and rice productivity. A one-season field experiment was conducted in Hydragric Anthrosols with four treatments: no fertilization (control), conventional chemical fertilization (CF), integrated application of biochar-based and chemical fertilizers (CBF), and biochar-based fertilizer alone (BF). Methane fluxes were monitored alongside soil physicochemical properties and the abundances of key functional microbial genes. Compared with CF, BF significantly reduced cumulative CH₄ emissions by 23.24% while maintaining comparable rice yield, resulting in a 28.67% reduction in yield-scaled CH₄ emissions. Biochar-based fertilization decreased dissolved organic carbon availability, buffered NH₄⁺-N concentrations, and increased soil pH. These changes shifted the microbial balance of CH₄ cycling, suppressing methanogenesis and enhancing methane oxidation, as reflected by a lower mcrA/pmoA ratio. Structural equation modeling indicated that CH₄ mitigation was jointly driven by reduced methanogenic activity and enhanced methane oxidation. Overall, biochar-based fertilization regulates soil chemical and microbial processes to mitigate CH₄ emissions without yield penalties, demonstrating strong potential as a scalable and field-applicable strategy for low-carbon rice production.